A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2024-05-23, 11:00 EDT
based on data in:
/scr/dings/PEVO/22_DNA_gencode_ref_new2/anne_vep/annotated
General Statistics
| Sample Name | Change rate | Ts/Tv | M Variants |
|---|---|---|---|
| chr1.imputed.poly_subset | 2495 | 2.431 | 0.10M |
SnpEff
5.2
SnpEff is a genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes). .DOI: 10.4161/fly.19695.
Variants by Genomic Region
The stacked bar plot shows locations of detected variants in the genome and the number of variants for each location.
The upstream and downstream interval size to detect these genomic regions is 5000bp by default.
Variant Effects by Impact
The stacked bar plot shows the putative impact of detected variants and the number of variants for each impact.
There are four levels of impacts predicted by SnpEff:
- High: High impact (like stop codon)
- Moderate: Middle impact (like same type of amino acid substitution)
- Low: Low impact (ie silence mutation)
- Modifier: No impact
Variants by Effect Types
The stacked bar plot shows the effect of variants at protein level and the number of variants for each effect type.
This plot shows the effect of variants with respect to the mRNA.
Variants by Functional Class
The stacked bar plot shows the effect of variants and the number of variants for each effect type.
This plot shows the effect of variants on the translation of the mRNA as protein. There are three possible cases:
- Silent: The amino acid does not change.
- Missense: The amino acid is different.
- Nonsense: The variant generates a stop codon.
VEP
VEP Ensembl VEP determines the effect of your variants on genes, transcripts and protein sequences, as well as regulatory regions.DOI: 10.1186/s13059-016-0974-4.
General Statistics
Table showing general statistics of VEP annotaion run
| Sample Name | Overlapped regulatory features | Overlapped transcripts | Overlapped genes | Variants filtered out | Variants processed |
|---|---|---|---|---|---|
| chr1.imputed.poly_subset | 0 | 2007 | 565 | 0 | 99933 |
Variant classes
Classes of variants found in the data.
Consequences
Predicted consequences of variations.
Variants by chromosome
Number of variants found on each chromosome.
Position in protein
Relative position of affected amino acids in protein.
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Software | Version |
|---|---|
| SnpEff | 5.2 |